Open Source S/R Medical Software

HeatmapGenerator is a graphical user interface software program written in C++, R, and OpenGL to create customized gene expression heatmaps from RNA-seq and microarray data in medical research. HeatmapGenerator can also be used to make heatmaps in a variety of other non-medical fields. HeatmapGenerator is peer-reviewed published software (http://www.scfbm.org/content/9/1/30). Please cite: [Khomtchouk et al.: "HeatmapGenerator: High performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline." Source Code for Biology and Medicine, 2014 9:30] HeatmapGenerator source code is available at: https://github.com/Bohdan-Khomtchouk/HeatmapGenerator Bohdan Khomtchouk wishes to acknowledge the support of the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. HeatmapGenerator is released under the GNU GPL.

These R packages are developed for data analysis of PK/PD modeling & simulation, bioequivalence/bioavailability (BE/BA), drug stability, in-vitro and in-vivo correlation (ivivc), as well as therapeutic drug monitoring (TDM).

Computer programs for application in Sports science, Physical Culture, among others. By Enrique R.P. Buendía Lozada. buendiaenr@gmail.com , Benemérita Universidad Autónoma de Puebla (BUAP), México. (Software without any warranty).

ClinStudyWeb is designed to provide a flexible infrastructure for managing patient and assay data from clinical studies. It uses a plugin system for study-specific web forms and arbitrarily complex test classifiers, and supports XML import/export.

Dissolution profile comparison (Biowaiver aid) Model Dependent-Independent Approach scripts for in-vitro dissolution profile comparison as proposed by Sathe et al. in 1996 (Sathe PM, Tsong Y, Shah VP. In-vitro dissolution profile comparison: statistics and analysis, model dependent approach. Pharm Res. 1996 Dec;13(12):1799-803) and Tsong et al. in 1996 (Tsong Y, Hammerstrom T, Sathe P, Shah VP. (1996) Statistical Assessment of Mean Differences between Two Dissolution Data Sets, Drug Info. J. 30:1105-1112).

Cancer registries need a tool to input, store, check and analyse their data. If these data are also coded and verified in a standard way, it facilitates the production of comparable analyses across registry populations. The main goal of the CanReg5 project is to provide a flexible and easy to use tool to accomplish these objectives. CanReg5 is a multi user, multi platform, open source tool to input, store, check and analyse cancer registry data. It has modules to do: data entry, quality control, consistency checks and basic analysis of the data It was designed with an emphasis on user friendliness, it has a modern user interface and is easy to navigate. Is available in several languages. (English, French, Spanish, Portuguese, Russian, Turkish, Georgian, and Chinese.)

Celsius is a data warehouse that provides web services for upload, archival, download, annotation, quantification, and normalization of all Affymetrix microarray platforms.

Chipster is a biologist-friendly analysis software for high-throughput data. It contains over 200 analysis tools for next generation sequencing (NGS), microarray and proteomics data. Users can combine tools in automatic analysis workflows, which can be shared. Chipster's interactive visualizations allow users to select datapoints and create new gene lists. For NGS data Chipster contains a built-in genome browser, which highlights SNPs and automatically indexes BAM files and calculates coverage. Chipster’s ability to provide a biologist-friendly access to a powerful analysis platform is technically based on a desktop application user interface, a flexible distributed architecture, and the ability to integrate many types of analysis tools (command line, R/Bioconductor, Java, Web Services etc). The platform is generic and easily extendable to other areas, even beyond bioinformatics. For more information, please see http://chipster.csc.fi and http://genomebiology.com/1471-2164/12/

GNUexp is a GNUstep/Cocoa framework and a collection of tools helping you to plan, develop, and administer applications associated with visual psychophysics, experimental psychology and statistical data analysis.

This is the sourceforge project supporting "Hackout: A hackathon for the analysis of disease outbreaks in R". It includes a repository for the collective development of the project's R package.

The simple program is a Witleaf handheld pulse oxymeter BIN file format data decoder. It reads BIN-files produced by popular professional pulse oxymeters manufactured by Shenzhen Witleaf Medical Electronics Co., Ltd. (like the WIT-S300 shown in the photo on the project icon) and produces a CSV-formatted output with the extracted data to stdout (gets printed to the console if not directed otherwise). More info on https://github.com/mrKirushko/OxyWitleaf2CSV .

This tool will allow individuals to find and quantify the overlap of variants with pseudogenic sequences.

A collection of code, bundled into a single R package, to perform several aspects of data management, image pre-processing, data analysis and statistical inference related to the quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI).

This application allow user to predict dissolution profile of solid dispersion systems based on algorithms like symbolic regression, deep neural networks, random forests or generalized boosted models. Those techniques can be combined to create expert system. Application was created as a part of project K/DSC/004290 subsidy for young researchers from Polish Ministry of Higher Education.

SPINA is software for the rapid, reliable and accurate determination of constant structure parameters of endocrine feedback control systems. It is a class of static function tests that require nothing more than steady-state concentrations of hormones or metabolites obtained in vivo. The first version of this cybernetic approach had been developed for the evaluation of the functional status of the thyroid gland, i.e. thyroid's secretory capacity (gain of thyroid, GT or SPINA-GT) and sum activity of peripheral deiodinases (GD or SPINA-GD). A second version has been established for insulin-glucose homeostasis. It delivers the secretory capacity of pancreatic beta cells (SPINA-GBeta), an estimate for the insulin receptor amplification (SPINA-GR) and a static disposition index as a measure for the loop gain of the feedback loop (SPINA-DI). Both implementations of SPINA have been validated in more than 50 clinical studies based on large cohorts.

This is the protein similarity network - PSIN. Here, the nodes are human proteins and they are linked only if they share considerable sequence similarity. We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do not hesitate to contact us in the forum or by email. Please see the original manuscript: Lopes, TJS, et al. (2015) - "Identifying problematic drugs based on the characteristics of their targets" - Frontiers in Pharmacology doi: 10.3389/fphar.2015.00186

XT-SDTM project move to CI-Reports project. Please visit the following CI-Reports project. http://sourceforge.net/projects/ci-reports/

Xpose - an S/R based population PK/PD model building aid for NONMEM.

Microarray analysis database

A R package for disease outbreak reconstruction using epidemiological and genetic data.

Shell script for spinal cord diffusion tensor imaging (DTI) preprocessing and outlier rejection.